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In Drosophila, a group of zinc finger architectural proteins recruits the CP190 protein to the chromatin, an interaction that is essential for the functional activity of promoters and insulators. In this study, we describe a new architectural C2H2 protein called Madf and Zinc-Finger Protein 1 (Mzfp1) that interacts with CP190. Mzfp1 has an unusual structure that includes six C2H2 domains organized in a C-terminal cluster and two tandem MADF domains. Mzfp1 predominantly binds to housekeeping gene promoters located in both euchromatin and heterochromatin genome regions. In vivo mutagenesis studies showed that Mzfp1 is an essential protein, and both MADF domains and the CP190 interaction region are required for its functional activity. The C2H2 cluster is sufficient for the specific binding of Mzfp1 to regulatory elements, while the second MADF domain is required for Mzfp1 recruitment to heterochromatin. Mzfp1 binds to the proximal part of the Fub boundary that separates regulatory domains of the Ubx and abd-A genes in the Bithorax complex. Mzfp1 participates in Fub functions in cooperation with the architectural proteins Pita and Su(Hw). Thus, Mzfp1 is a new architectural C2H2 protein involved in the organization of active promoters and insulators in Drosophila.
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Proteínas de Drosophila , Drosophila melanogaster , Elementos Aisladores , Proteínas Nucleares , Regiones Promotoras Genéticas , Animales , Proteínas de Drosophila/metabolismo , Proteínas de Drosophila/genética , Elementos Aisladores/genética , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Proteínas Nucleares/metabolismo , Proteínas Nucleares/genética , Heterocromatina/metabolismo , Heterocromatina/genética , Genes Esenciales , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Unión Proteica , Regulación de la Expresión Génica , Eucromatina/metabolismo , Eucromatina/genética , Proteínas de Unión al ADN/metabolismo , Proteínas de Unión al ADN/genética , Proteínas Asociadas a MicrotúbulosRESUMEN
The production of experimental beer and cider products has increased, worldwide. The complex microbiomes found in these beverages affect their organoleptic qualities and chemical compositions and can have diverse impacts on human health. The total diversity of a microbiome can be elucidated through the use of high-throughput sequencing and comprehensive data analysis tools. We analysed the bacterial and yeast microbiomes found in mixed and spontaneously fermented beers (n = 14) and unpasteurised apple ciders (n = 6), using high-throughput 16S rRNA and internal transcribed spacer (ITS) sequencing. The ratio of bacteria to yeast was measured using quantitative polymerase chain reaction (qPCR), and short-chain organic acids were analysed using high-performance liquid chromatography (HPLC). An upgraded version of the Knomics-Biota system was used to analyse the data. The microbiomes included both starter microorganisms and those that originate from the production environment and the raw materials. In addition to the common Saccharomyces and Brettanomyces, the yeast diversity included many non-conventional species. The bacterial community in beer was dominated by Lactobacillus species, whereas these communities were more diverse in cider. Lactobacillus acetotolerans was prevalent in wild ales, whereas Candida ethanolica was prevalent in cask-matured beverages. We observed complex patterns of subspecies-level yeast diversity across beer styles, breweries, and countries. Our study represents an exploratory analysis of non-conventional beer and cider microbiomes and metabolomes, which contributes information necessary to develop improved quality control processes and may drive innovative product development in experimental and artisanal brewing.
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Bebidas Alcohólicas/microbiología , Bacterias/aislamiento & purificación , Bebidas Alcohólicas/análisis , Bacterias/clasificación , Bacterias/genética , Bacterias/metabolismo , Cerveza/análisis , Cerveza/microbiología , Fermentación , Microbiología de Alimentos , Malus/microbiología , Microbiota , Levaduras/clasificación , Levaduras/genética , Levaduras/aislamiento & purificación , Levaduras/metabolismoRESUMEN
Transcription activation factors and multisubunit coactivator complexes get recruited at specific chromatin sites via protein domains that recognize histone modifications. Single PHDs (plant homeodomains) interact with differentially modified H3 histone tails. Double PHD finger (DPF) domains possess a unique structure different from PHD and are found in six proteins: histone acetyltransferases MOZ and MORF; chromatin remodeling complex BAF (DPF1-3); and chromatin remodeling complex PBAF (PHF10). Among them, PHF10 stands out due to the DPF sequence, structure, and functions. PHF10 is ubiquitously expressed in developing and adult organisms as four isoforms differing in structure (the presence or absence of DPF) and transcription regulation functions. Despite the importance of the DPF domain of PHF10 for transcription activation, its structure remains undetermined. We performed homology modeling of the human PHF10 DPF domain and determined common and distinct features in structure and histone modifications recognition capabilities, which can affect PBAF complex chromatin recruitment. We also traced the evolution of DPF1-3 and PHF10 genes from unicellular to vertebrate organisms. The data reviewed suggest that the DPF domain of PHF10 plays an important role in SWI/SNF-dependent chromatin remodeling during transcription activation.
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Ensamble y Desensamble de Cromatina/genética , Proteínas de Homeodominio , Proteínas de Neoplasias , Dedos de Zinc PHD/genética , Animales , Secuencia Conservada , Evolución Molecular , Duplicación de Gen , Histonas/metabolismo , Proteínas de Homeodominio/química , Proteínas de Homeodominio/genética , Proteínas de Homeodominio/metabolismo , Humanos , Proteínas de Neoplasias/química , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Subunidades de Proteína/química , Subunidades de Proteína/genética , Subunidades de Proteína/metabolismo , Activación TranscripcionalRESUMEN
Nowadays the advent of innovative high-throughput sequencing allows obtaining high-quality microbiome profiling. However, PCR-based tests are still considered the "golden standard" for many clinical applications. Here, we designed a qPCR-based platform with fluorescent-labeled oligonucleotide probes for assessing human gut microbiome composition. The system allows conducting qualitative and semiquantitative analysis for 12 prokaryotic taxa that are prevalent in the human gut and associated with diseases, diet, age and other factors. The platform was validated by comparing microbiome profile data obtained with two different methods - the platform and high-throughput 16S rRNA sequencing - across 42 stool samples. The test can form the basis for precise and cost-efficient microbiome assay for large-scale surveys including clinical trials with interventions related to diet and disease risks.
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Microbioma Gastrointestinal/genética , Filogenia , Reacción en Cadena de la Polimerasa/métodos , Cartilla de ADN/metabolismo , Sondas de ADN/metabolismo , Heces/microbiología , Secuenciación de Nucleótidos de Alto Rendimiento , ARN Ribosómico 16S/genéticaRESUMEN
BACKGROUND: High serum levels of certain aromatic microbial metabolites (AMM) are associated with severity and mortality in critically ill patients. Omics-based studies suggest gut dysbiosis and reduced microbiome diversity in critical conditions. However, the landscape of gut microbial metabolites is still to be outlined, not to mention the interplay correlation between the metabolome and gut microbiome in critically ill patients. The aim of this study was to analyze the association between serum and fecal levels of AMM and compare them with the composition of gut microbiota in critically ill patients in the acute and chronic stages. METHODS: In this prospective observational pilot study, we analyzed the temporal dynamics of the gut microbiome and the AMM spectrum across two distinct subgroups-acute critical ill (ACI) patients with nosocomial pneumonia and chronically critically ill (CCI) patients (9 subjects each group)-as well as performed comparison with 23 healthy volunteers. The AMM levels for each patient were measured using GC-MS in simultaneously taken serum and fecal samples (SFS). These parameters were compared with 16S rRNA fecal microbiome profiles. RESULTS: The observed proportions of bacterial taxa suggest a significant gut dysbiosis in the ACI and the CCI patients. Stronger imbalance in microbiome composition and dynamics observed in the ACI patients compared to the CCI ones resonates with a higher severity in the former group. The total levels of AMM in serum samples were higher for the ACI patients than for the CCI patients (3.7 (1.4-6.3) and 1.1 (1.0-1.6) µM, respectively; p = 0.0003). The qualitative composition of the SFS was also altered. We discovered significant associations between gut microbial taxa levels and metabolite concentrations in blood serum as well as in feces in each of the ACI and the CCI patients. CONCLUSIONS: Aromatic microbial metabolite profiles in the gut and the serum are interlinked and reflect a disruption of the gut microbial community in critically ill patients.
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Enfermedad Crítica , Disbiosis/microbiología , Heces/microbiología , Suero/microbiología , Microbioma Gastrointestinal/inmunología , Microbioma Gastrointestinal/fisiología , Humanos , Proyectos Piloto , Estudios ProspectivosRESUMEN
BACKGROUND: CTCF is highly likely to be the ancestor of proteins that contain large clusters of C2H2 zinc finger domains, and its conservation is observed across most bilaterian organisms. In mammals, CTCF is the primary architectural protein involved in organizing chromosome topology and mediating enhancer-promoter interactions over long distances. In Drosophila, CTCF (dCTCF) cooperates with other architectural proteins to establish long-range interactions and chromatin boundaries. CTCFs of various organisms contain an unstructured N-terminal dimerization domain (DD) and clusters comprising eleven zinc-finger domains of the C2H2 type. The Drosophila (dCTCF) and human (hCTCF) CTCFs share sequence homology in only five C2H2 domains that specifically bind to a conserved 15 bp motif. RESULTS: Previously, we demonstrated that CTCFs from different organisms carry unstructured N-terminal dimerization domains (DDs) that lack sequence homology. Here we used the CTCFattP(mCh) platform to introduce desired changes in the Drosophila CTCF gene and generated a series of transgenic lines expressing dCTCF with different variants of the N-terminal domain. Our findings revealed that the functionality of dCTCF is significantly affected by the deletion of the N-terminal DD. Additionally, we observed a strong impact on the binding of the dCTCF mutant to chromatin upon deletion of the DD. However, chromatin binding was restored in transgenic flies expressing a chimeric CTCF protein with the DD of hCTCF. Although the chimeric protein exhibited lower expression levels than those of the dCTCF variants, it efficiently bound to chromatin similarly to the wild type (wt) protein. CONCLUSIONS: Our findings suggest that one of the evolutionarily conserved functions of the unstructured N-terminal dimerization domain is to recruit dCTCF to its genomic sites in vivo.
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Proteínas de Drosophila , Drosophila , Animales , Humanos , Animales Modificados Genéticamente/metabolismo , Factor de Unión a CCCTC/metabolismo , Cromatina/metabolismo , Dimerización , Drosophila/genética , Drosophila melanogaster/genética , Proteínas de Drosophila/metabolismo , Mamíferos/genéticaRESUMEN
The gut microbiome plays a pivotal role in the human body, and perturbations in its composition have been linked to various disorders. Stability is an essential property of a healthy human gut microbiome, which allows it to maintain its functional richness under the external influences. This property has been explored through two distinct methodologies - mathematical modelling based on ecological principles and statistical analysis drawn from observations in interventional studies. Here we conducted a meta-analysis aimed to compare the two approaches utilising the data from 9 interventional and time series studies encompassing 3512 gut microbiome profiles obtained via 16S rRNA gene sequencing. By employing the previously published compositional Lotka-Volterra method, we modelled the dynamics of the microbial community and evaluated ecological stability measures. These measures were compared to those based on observed microbiome changes. There was a substantial correlation between the outcomes of the two approaches. Particularly, local stability assessed within the ecological paradigm was positively correlated with observational stability measures accounting for the compositional nature of microbiome data. Additionally, we were able to reproduce the previously reported inverse relationship between the community's robustness to microorganism loss and local stability, attributed to the distinct impacts of coefficient characterising the network decomposition on these two stability assessments. Our findings demonstrate harmonisation between the ecological and observational approaches to microbiome analysis, advancing the understanding of healthy gut microbiome concept. This paves the way to develop efficient microbiome-targeting interventions for disease prevention and treatment.
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The composition of the gut microbiome stores the imprints of prior infections and other impacts. COVID-19 can cause changes in inflammatory status that persist for a considerable time after infection ends. As the gut microbiome is closely associated with immunity and inflammation, the infection severity might be linked to its community structure dynamics. Using 16S rRNA sequencing of stool samples, we investigated the microbiome three months after the end of the disease/infection or SARS-CoV-2 contact in 178 post-COVID-19 patients and those who contacted SARS-CoV-2 but were not infected. The cohort included 3 groups: asymptomatic subjects (n = 48), subjects who contacted COVID-19 patients with no further infection (n = 46), and severe patients (n = 86). Using a novel compositional statistical algorithm (nearest balance) and the concept of bacterial co-occurrence clusters (coops), we compared microbiome compositions between the groups as well as with multiple categories of clinical parameters including: immunity, cardiovascular parameters and markers of endothelial dysfunction, and blood metabolites. Although a number of clinical indicators varied drastically across the three groups, no differences in microbiome features were identified between them at this follow-up point. However, there were multiple associations between the microbiome features and clinical data. Among the immunity parameters, the relative lymphocyte number was linked to a balance including 14 genera. Cardiovascular parameters were associated with up to four bacterial cooperatives. Intercellular adhesion molecule 1 was linked to a balance including ten genera and one cooperative. Among the blood biochemistry parameters, calcium was the only parameter associated with the microbiome via a balance of 16 genera. Our results suggest comparable recovery of the gut community structure in the post-COVID-19 period, independently of severity or infection status. The multiple identified associations of clinical analysis data with the microbiome provide hypotheses about the participation of specific taxa in regulating immunity and homeostasis of cardiovascular and other body systems in health, as well as their disruption in SARS-CoV-2 infections and other diseases.
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Linking microbiome composition obtained from metagenomic or 16S rRNA sequencing to various factors poses a real challenge. The compositional approach to such data is well described: a so-called isometric log-ratio (ILR) transform provides correct treatment of relative abundances. Most existing compositional methods differ in the particular choice of the transform. Although this choice does not influence the prediction of a model, it determines the subset of balances between groups of microbial taxa subsequently used for interpreting the composition shifts. We propose a method to interpret these shifts independently of the initial choice of ILR coordinates by the nearest single-balance shift. We describe here application of the method to regression, classification, and principal balance analysis of compositional data. Analytical treatment and cross-validation show that the approach provides the least-squares estimate of a single-balance shift associated with a factor with possible adjustment for covariates. As for classification and principal balance analysis, the nearest balance method provides results comparable to other compositional tools. Its advantages are the absence of assumptions about the number of taxa included in the balance and its low computational cost. The method is implemented in the R package NearestBalance. IMPORTANCE The method proposed here extends the range of compositional methods providing interpretation of classical statistical tools applied to data converted to the ILR coordinates. It provides a strictly optimal solution in several special cases. The approach is universally applicable to compositional data of any nature, including microbiome data sets.
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Microbiota , ARN Ribosómico 16S/genética , Microbiota/genética , Metagenómica/métodos , Metagenoma , Grupo SocialRESUMEN
Maintaining equilibrium of the gut microbiome is crucial for human health. Diet represents an important and generally accessible natural channel of controlling the nutrients supply to the intestinal microorganisms. Although many studies showed that dietary interventions can specifically modulate gut microbiome composition, further progress of the approach is complicated by interindividual variability of the microbial community response. The reported causes of this variability include the baseline microbiome composition features, but it is unclear whether any of them are intervention-specific. Here, we applied a unified computational framework to investigate the variability of microbiome response measured as beta diversity in eight various dietary interventions using previously published 16S rRNA sequencing datasets. We revealed a number of baseline microbiome features which determine the microbiome response in an intervention-independent manner. One of the most stable associations, reproducible for different interventions and enterotypes, was a negative dependence of the response on the average number of genes per microorganism in the community-an indicator of the community functional redundancy. Meanwhile, many revealed microbiome response determinants were enterotype-specific. In Bact1 and Rum enterotypes, the response was negatively correlated with the baseline abundance of their main drivers. Additionally, we proposed a method for preliminary assessment of the microbiome response. Our study delineats the universal features determining microbiome response to diverse interventions. The proposed approach is promising for understanding the mechanisms of gut microbiome stability and improving the efficacy of personalised microbiome-tailored interventions.
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Microbioma Gastrointestinal , Microbiota , Dieta , Heces , Humanos , ARN Ribosómico 16S/genéticaRESUMEN
Colorectal cancer is the third most commonly diagnosed cancer worldwide. Human gut microbiome plays important roles in protecting against it, as well as contributing to its onset and progression. Identification of specific bacterial taxa associated with early stages of colorectal cancer may help develop effective microbiome-based diagnostics. For precancerous lesions, links of their characteristics to luminal and tumor-associated microbiome composition are to be elucidated. Paired stool and tumor brush biopsy samples were collected from 50 patients with precancerous lesions and early forms of colon cancer; their microbial communities were profiled using high-throughput 16S rRNA sequencing. We showed that the microbiome differences between stool and biopsy samples can be to a high extent computationally corrected. Compositionality-aware statistical analysis of microbiome composition revealed its associations with the number of lesions, lesion type, location and malignization pathway. A major determinant of precancerous lesions malignancy risk-the number of lesions-was positively associated with the abundance of H2S-producing taxa. Our results contribute to the basis for developing early non-invasive colorectal cancer diagnostics via identifying microorganisms likely participating in early stages of cancer pathogenesis.
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Eating less meat is increasingly seen as a healthier, more ethical option. This is leading to growing numbers of flexitarian consumers looking for plant-based meat alternatives (PBMAs) to replace at least some of the animal meat they consume. Popular PBMA products amongst flexitarians, including plant-based mince, burgers, sausages and meatballs, are often perceived as low-quality, ultra-processed foods. However, we argue that the mere industrial processing of ingredients of plant origin does not make a PBMA product ultra-processed by default. To test our hypothesis, we conducted a randomised controlled trial to assess the changes to the gut microbiota of a group of 20 participants who replaced several meat-containing meals per week with meals cooked with PBMA products and compared these changes to those experienced by a size-matched control. Stool samples were subjected to 16S rRNA sequencing. The resulting raw data was analysed in a compositionality-aware manner, using a range of innovative bioinformatic methods. Noteworthy changes included an increase in butyrate metabolising potential-chiefly in the 4-aminobutyrate/succinate and glutarate pathways-and in the joint abundance of butyrate-producing taxa in the intervention group compared to control. We also observed a decrease in the Tenericutes phylum in the intervention group and an increase in the control group. Based on our findings, we concluded that the occasional replacement of animal meat with PBMA products seen in flexitarian dietary patterns can promote positive changes in the gut microbiome of consumers.
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CTCF is the most likely ancestor of proteins that contain large clusters of C2H2 zinc finger domains (C2H2) and is conserved among most bilateral organisms. In mammals, CTCF functions as the main architectural protein involved in the organization of topology-associated domains (TADs). In vertebrates and Drosophila, CTCF is involved in the regulation of homeotic genes. Previously, it was found that null mutations in the dCTCF gene died as pharate adults, which failed to eclose from their pupal case, or shortly after hatching of adults. Here, we obtained several new null dCTCF mutations and found that the complete inactivation of dCTCF appears is limited mainly to phenotypic manifestations of the Abd-B gene and fertility of adult flies. Many modifiers that are not associated with an independent phenotypic manifestation can significantly enhance the expressivity of the null dCTCF mutations, indicating that other architectural proteins are able to functionally compensate for dCTCF inactivation in Drosophila. We also mapped the 715-735 aa region of dCTCF as being essential for the interaction with the BTB (Broad-Complex, Tramtrack, and Bric a brac) and microtubule-targeting (M) domains of the CP190 protein, which binds to many architectural proteins. However, the mutational analysis showed that the interaction with CP190 was not important for the functional activity of dCTCF in vivo.
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Factor de Unión a CCCTC/fisiología , Proteínas de Drosophila/fisiología , Animales , Factor de Unión a CCCTC/química , Factor de Unión a CCCTC/genética , Factor de Unión a CCCTC/metabolismo , Cromatina/metabolismo , Drosophila/genética , Proteínas de Drosophila/química , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Femenino , Infertilidad/genética , Masculino , Proteínas Asociadas a Microtúbulos/metabolismo , Proteínas Nucleares/metabolismo , Dominios y Motivos de Interacción de ProteínasRESUMEN
The community structure and metabolic potential of gut microbiome is not well investigated, especially in chronically critically ill patients with prolonged dependence on support systems after severe brain disorders. Microbial phenolic metabolites can target the brain function by the direct and indirect modulation of inflammation. The aim of this study was to investigate the features of the gut microbiota and profile of certain metabolites in the progression and reversibility of neurological disorders in chronically critically ill patients. Fecal samples were collected in dynamics from such patients (n = 44) and analyzed using 16S rRNA sequencing. Serum microbial and mitochondrial metabolites were measured by GC-MS and compared with the biomarkers and clinical neurological scores. The identified associations between specific bacterial taxa in fecal samples, neurological status and serum levels of metabolites suggest that impacts on specific members of the gut microbiota and their metabolism might be a promising tool for regulating brain function in future.
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Aim: To reveal the relationship between gut microbiota composition and subfractional spectrum of serum lipoproteins and metabolic markers in healthy individuals from Moscow. Methods: The study included 304 participants (104 were men), who underwent thorough preclinical assessment to exclude any chronic disease as well as cardiovascular pathology. Lipoprotein subfractional distribution was analyzed by Lipoprint LDL System (Quantimetrix, Redodno Beach, CA, USA). Gut microbiota composition was assessed by 16S rRNA sequencing of V3-V4 regions. Results: High gut microbiota diversity was positively associated with HDL-cholesterol (C) level and negatively associated with abdominal obesity, BMI, and dyslipidemia. According to selbal analysis, excessive representation of Prevotella spp. was positively associated with IDL-C and LDL-2-C. VLDL-C correlated with Ruminococcus_u/Faecalibacterium_prausnitzii balance. An unexpected positive relationship between LDL-C level and Bifidobacteriaceae_u/Christensenellaceae_u to Bifidobacterium_u balance was found, which may reflect the importance of the integrative microbiota assessment. Low microbiota diversity was associated with obesity, abdominal obesity and low HDL-C level. Conclusions: Gut microbiota imbalance may be one of the components involved in metabolic disorders. The balance of microorganisms and the microbiota diversity may play a more significant role in human health than individual bacterial genera.
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BACKGROUND: Pita is required for Drosophila development and binds specifically to a long motif in active promoters and insulators. Pita belongs to the Drosophila family of zinc-finger architectural proteins, which also includes Su(Hw) and the conserved among higher eukaryotes CTCF. The architectural proteins maintain the active state of regulatory elements and the long-distance interactions between them. In particular, Pita is involved in the formation of several boundaries between regulatory domains that controlled the expression of three hox genes in the Bithorax complex (BX-C). The CP190 protein is recruited to chromatin through interaction with the architectural proteins. RESULTS: Using in vitro pull-down analysis, we precisely mapped two unstructured regions of Pita that interact with the BTB domain of CP190. Then we constructed transgenic lines expressing the Pita protein of the wild-type and mutant variants lacking CP190-interacting regions. We have demonstrated that CP190-interacting region of the Pita can maintain nucleosome-free open chromatin and is critical for Pita-mediated enhancer blocking activity in BX-C. At the same time, interaction with CP190 is not required for the in vivo function of the mutant Pita protein, which binds to the same regions of the genome as the wild-type protein. Unexpectedly, we found that CP190 was still associated with the most of genome regions bound by the mutant Pita protein, which suggested that other architectural proteins were continuing to recruit CP190 to these regions. CONCLUSIONS: The results directly demonstrate role of CP190 in insulation and support a model in which the regulatory elements are composed of combinations of binding sites that interact with several architectural proteins with similar functions.
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Proteínas de Unión al ADN/metabolismo , Proteínas de Drosophila/metabolismo , Drosophila melanogaster , Proteínas Asociadas a Microtúbulos/metabolismo , Proteínas Nucleares/metabolismo , Factores de Transcripción/metabolismo , Animales , Proteínas de Unión al ADN/genética , Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Elementos Aisladores , Proteínas Asociadas a Microtúbulos/genética , Proteínas Nucleares/genética , Factores de Transcripción/genéticaRESUMEN
We studied the repression of adult and embryo-larval genes of the major globin gene locus in D. rerio fibroblasts. The results obtained suggest that at least some of the globin genes are repressed by Polycomb, similarly to human α-globin genes. Furthermore, within two α/ß globin gene pairs, repression of α-type and ß-type genes appears to be mediated by different mechanisms, as increasing the level of histone acetylation can activate transcription of only ß-type genes.
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Transcripción Genética , Proteínas de Pez Cebra/biosíntesis , Pez Cebra/metabolismo , Globinas alfa/biosíntesis , Globinas beta/biosíntesis , Animales , Pez Cebra/genética , Proteínas de Pez Cebra/genética , Globinas alfa/genética , Globinas beta/genéticaRESUMEN
Recently, the concept has arisen that a special class of architectural proteins exists, which are responsible not only for global chromosome architecture but also for the local regulation of enhancer-promoter interactions. Here, we describe a new architectural protein, with a total size of only 375 aa, which contains an N-terminal zinc finger-associated domain (ZAD) and a cluster of five zinc finger C2H2 domains at the C-terminus. This new protein, named ZAD and Architectural Function 1 protein (ZAF1 protein), is weakly and ubiquitously expressed, with the highest expression levels observed in oocytes and embryos. The cluster of C2H2 domains recognizes a specific 15-bp consensus site, located predominantly in promoters, near transcription start sites. The expression of ZAF1 by a tissue-specific promoter led to the complete blocking of the eye enhancer when clusters of ZAF1 binding sites flanked the eye enhancer in transgenic lines, suggesting that the loop formed by the ZAF1 protein leads to insulation. The ZAF1 protein also supported long-range interactions between the yeast GAL4 activator and the white promoter in transgenic Drosophila lines. A mutant protein lacking the ZAD failed to block the eye enhancer or to support distance interactions in transgenic lines. Taken together, these results suggest that ZAF1 is a minimal architectural protein that can be used to create a convenient model for studying the mechanisms of distance interactions.
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Proteínas de Unión al ADN/metabolismo , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/genética , Proteínas Nucleares/metabolismo , Factores Generales de Transcripción/metabolismo , Transportadoras de Casetes de Unión a ATP/genética , Animales , Animales Modificados Genéticamente , Sitios de Unión , Proteínas de Unión al ADN/química , Proteínas de Drosophila/química , Proteínas de Drosophila/genética , Drosophila melanogaster/metabolismo , Embrión no Mamífero/metabolismo , Elementos de Facilitación Genéticos , Ojo/metabolismo , Proteínas del Ojo/genética , Proteínas Nucleares/química , Proteínas Nucleares/genética , Regiones Promotoras Genéticas , Factores de Transcripción/metabolismo , Factores Generales de Transcripción/química , Factores Generales de Transcripción/genética , Dedos de ZincRESUMEN
The gut microbiome is of utmost importance to human health. While a healthy microbiome can be represented by a variety of structures, its functional capacity appears to be more important. Gene content of the community can be assessed by "shotgun" metagenomics, but this approach is still too expensive. High-throughput amplicon-based surveys are a method of choice for large-scale surveys of links between microbiome, diseases, and diet, but the algorithms for predicting functional composition need to be improved to achieve good precision. Here we show how feature engineering based on microbial phenotypes, an advanced method for functional prediction from 16S rRNA sequencing data, improves identification of alterations of the gut microbiome linked to the disease. We processed a large collection of published gut microbial datasets of inflammatory bowel disease (IBD) patients to derive their community phenotype indices (CPI)-high-precision semiquantitative profiles aggregating metabolic potential of the community members based on genome-wide metabolic reconstructions. The list of selected metabolic functions included metabolism of short-chain fatty acids, vitamins, and carbohydrates. The machine-learning approach based on microbial phenotypes allows us to distinguish the microbiome profiles of healthy controls from patients with Crohn's disease and from ones with ulcerative colitis. The classifiers were comparable in quality to conventional taxonomy-based classifiers but provided new findings giving insights into possible mechanisms of pathogenesis. Feature-wise partial dependence plot (PDP) analysis of contribution to the classification result revealed a diversity of patterns. These observations suggest a constructive basis for defining functional homeostasis of the healthy human gut microbiome. The developed features are promising interpretable candidate biomarkers for assessing microbiome contribution to disease risk for the purposes of personalized medicine and clinical trials.
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Intestinal microbiota play a considerable role in the host's organism, broadly affecting its organs and tissues. The kidney can also be the target of the microbiome and its metabolites (especially short-chain fatty acids), which can influence renal tissue, both by direct action and through modulation of the immune response. This impact is crucial, especially during kidney injury, because the modulation of inflammation or reparative processes could affect the severity of the resulting damage or recovery of kidney function. In this study, we compared the composition of rat gut microbiota with its outcome, in experimental acute ischemic kidney injury and named the bacterial taxa that play putatively negative or positive roles in the progression of ischemic kidney injury. We investigated the link between serum creatinine, urea, and a number of metabolites (acylcarnitines and amino acids), and the relative abundance of various bacterial taxa in rat feces. Our analysis revealed an increase in levels of 32 acylcarnitines in serum, after renal ischemia/reperfusion and correlation with creatinine and urea, while levels of three amino acids (tyrosine, tryptophan, and proline) had decreased. We detected associations between bacterial abundance and metabolite levels, using a compositionality-aware approach-Rothia and Staphylococcus levels were positively associated with creatinine and urea levels, respectively. Our findings indicate that the gut microbial community contains specific members whose presence might ameliorate or, on the contrary, aggravate ischemic kidney injury. These bacterial taxa could present perspective targets for therapeutical interventions in kidney pathologies, including acute kidney injury.